Structure-Based Design and Synthesis of a Potent Matrix

Publication Date (Web): May 27, 2000. Copyright © 2000 American Chemical ... J. T. Hyland , Simon E. Ward. Chemical Communications 2005 (27), 3439 ...
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© Copyright 2000 by the American Chemical Society

Volume 43, Number 12

June 15, 2000

Communications to the Editor Structure-Based Design and Synthesis of a Potent Matrix Metalloproteinase-13 Inhibitor Based on a Pyrrolidinone Scaffold Ralph P. Robinson,* Ellen R. Laird, James F. Blake, Jon Bordner, Kathleen M. Donahue, Lori L. Lopresti-Morrow, Peter G. Mitchell, Matthew R. Reese, Lisa M. Reeves, Ethan J. Stam, and Sue A. Yocum Central Research Division, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340 Received March 23, 2000

Introduction. The inhibition of matrix metalloproteinases (MMPs) is an attractive approach toward the treatment of a variety of diseases.1-3 For example, inhibitors of MMP-2 and MMP-9 are sought for prevention of cancer tumor growth,4 while inhibitors of MMP13 show potential for reducing cartilage loss in osteoarthritis.5 Several MMP inhibitors are now in advanced clinical trials. However, there remains considerable room for optimization of oral absorption and duration of action while maintaining potency and selectivity. The vast majority of reported MMP inhibitors can be viewed as being derivatives of either the substrate-like peptidic motif 1 (e.g., marimistat, 2) or the aryl sulfonamidebased hydroxamic acids 3 (e.g., CGS 27023A, 4).6 Although substantial modification of 1 and 3 is often tolerated, the discovery of new structural classes should prove valuable in the search for clinically useful MMP inhibitors. We now describe the structure-based design and synthesis of a novel, potent, and selective inhibitor of MMP-13 that utilizes a pyrrolidinone ring as a scaffold.7 Results and Discussion. X-ray crystal structures of MMPs (including MMP-13) with bound inhibitors reveal that inhibitor binding interactions typically include coordination of the active site Zn atom by a ligand (e.g., hydroxamic acid) and occupancy of the S1′ pocket with a hydrophobic group.8-14 Another interaction often

observed involves hydrogen bonding between an acceptor on the inhibitor and main chain NHs of amino acid residues flanking the catalytic site, specifically Leu-185 and Ala-186 (MMP-13 numbering). A few inhibitors also possess a proton donor that interacts with Ala-186.8,10 The close proximity of the latter two interaction sites led us to consider lactams that could make both hydrogen bond-donating and -accepting contacts and, being cyclic, would possess the entropic advantage of ring constraint. Using a homology model of the catalytic domain of MMP-13 based on the X-ray structure of MMP-8,15,16 five- and six-membered ring lactams were examined to identify the position most favorable for attaching a ligand for the active site Zn atom. Among the various possibilities, the pyrrolidin-5-one 5 bearing hydroxamate at the 2-position was especially attractive (Chart 1). As determined using a Monte Carlo fragment positioning algorithm,17 this structure is able to adopt an energetically favorable orientation capable of directChart 1

* To whom correspondence should be addressed. Tel: 860-441-4923. Fax: 860-715-2469. E-mail: [email protected].

10.1021/jm0001368 CCC: $19.00 © 2000 American Chemical Society Published on Web 05/27/2000

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Scheme 1a

a Reagents: (a) I , pyridine, CCl (31%); (b) 4-MeO(C H )B(OH) , cat. Pd(PPh ) , aq Na CO , toluene, 4 (77%); (c) H (3 atm), 20% 2 4 6 4 2 3 4 2 3 2 Pd(OH)2/C, EtOH (100%); (d) aq 0.5 M HCl (1 equiv), THF (48%); (e) H5IO6, cat. CrO3, wet CH3CN/0 °C (98%); (f) PhCH2ONH2‚HCl, BOP, i-Pr2NEt, CH2Cl2 (73%); (g) HCl(g)/CH2Cl2 (80%); (h) H2 (3 atm), 5% Pd/BaSO4, MeOH (96%).

ing a group (R) from the cis 4-position into the S1′ pocket as in 6 (Chart 1; see also Figure 1).

Figure 1. Model of binding mode for compound 6b in the active site of MMP-13. The protein is rendered as a solventaccessible surface and is clipped to reveal the S1′ pocket. The catalytic zinc is portrayed as a space-filled violet sphere.

On the basis of the reported MMP binding mode of 4 and related aryl sulfone analogues (in which an aryl group fills the S1′ pocket),14,18 as well as the availability of starting materials, compound 6a (R ) 4-methoxyphenyl) was first prepared. The synthesis began with the R,β-unsaturated γ-lactam 719 which was R-iodinated20 to obtain 8 (Scheme 1). Suzuki coupling21 introduced the 4-methoxyphenyl group, providing 9,22 and hydrogenation, giving 10, established the cis relationship required between the substituents on the pyrrolidinone ring.23 Selective removal of the tert-butyldimethylsilyl protecting group24 and oxidation of the intermediate alcohol25 gave the carboxylic acid 11. Final conversion to 6a was carried out in three steps involving coupling to O-benzylhydroxylamine and removal of the BOC and benzyl26 protecting groups. Testing of 6a against MMP-13 showed the compound to have modest activity (IC50 ) 1480 nM, Table 1). This result suggested that the pyrrolidinone scaffold could be functioning as proposed and that appropriate substitution of the phenyl ring with larger hydrophobic groups might improve potency by filling the S1′ pocket more completely. Accordingly, compounds 6b-f were prepared by routes paralleling that in Scheme 1.27 On the basis of the reported SAR among analogues of 3, as

well as docking studies using the MMP-13 homology model, the 4-(4-fluorophenoxy)phenyl compound 6b was of particular interest (Figure 1). Indeed, this compound exhibited high potency against MMP-13 (IC50 ) 7 nM). As for 6a, inhibition of MMP-1 by 6b was weak, a potentially desirable result in consideration of side effects attributed to MMP-1 inhibition by “broadspectrum” MMP inhibitors.4 Additionally, 6b showed modest to high selectivity for MMP-13 versus MMP-2, MMP-3, and MMP-9 (Table 2). Because the pyrrolidinones 6 are conformationally restricted, it was expected that the potency of a given analogue against various MMPs would be particularly dependent on the degree to which the enzyme must reorganize (or its capacity to do so) upon ligand binding. Insofar as the S1′ site involves a large area of interaction, the involvement of amino acid residues defining this pocket is particularly relevant. The observation that 6b is a very potent inhibitor of MMP-13 suggests that the residues comprising the MMP-13 S1′ pocket are preorganized to accept this inhibitor without requiring energetically demanding movement. For the other MMPs, residues that may affect access to (or the flexibility of) the S1′ pocket can be identified to explain the decreases in the activity of 6b. In MMP-1, an arginine side chain (Arg-214) residing within S1′ normally blocks large groups from entry resulting in a preference by MMP-1 for small P1′ substituents. Although in some cases large hydrophobic groups such as a diphenyl ether can be accommodated by displacement of Arg-214, binding potency is often reduced.14 Similarly, in MMP-3, a tyrosine side chain (Tyr-223) has been observed to restrict access to S1′.28 In MMP-2 and MMP-9 there are fewer residues in the loop linking helices B and C that forms part of S1′.29 Therefore, the loop may be less flexible and so may be more restricted in accommodating rigid ligands. Compounds 6c-f were significantly less potent (at least ∼25-fold) than 6b against MMP-13 (Table 1). The tight SAR is consistent with occupation of a well-defined pocket such as the S1′ site. An examination of 6c and 6d within the homology model shows that although the aryl substituents can be accommodated, they are less complementary than the naturally bent 4-(4-fluorophenoxy)phenyl group of 6b (Figure 1). The 4-benzyloxyphenyl group of 6e exhibits a similar geometry to 6b, and therefore, the modest potency of 6e against MMP13 is surprising. The low potency of 6f is consistent with

Communications to the Editor

Journal of Medicinal Chemistry, 2000, Vol. 43, No. 12 2295

Table 1. Inhibition of MMP-1 and MMP-13 by 6a-f, 12, and 13

a

Values are (SD of 3 determinations unless otherwise noted (n).

Table 2. Inhibition of Various MMPs by 6b

a

enzyme

IC50 (nM)a

MMP-1 MMP-2 MMP-3 MMP-9 MMP-13

1560 ( 120 39 ( 17 703 ( 170 82 ( 16 7(1

Values are (SD of 3 determinations.

the model since a poor fit of the 3-(4-fluorophenoxy)phenyl group within S1′ is predicted. As expected, the trans (2R,4R) compound 1230 was considerably less potent versus MMP-13 (IC50 ) 3390 nM) than its cis stereoisomer 6b. The carboxylate analogue of 6b (13)31 was devoid of MMP-13 activity in keeping with the SAR in other series where the carboxylates possess markedly less MMP inhibitory activity than the corresponding hydroxamates. Conclusion. In summary, we have discovered a potent inhibitor of MMP-13 by a structure-based approach using a homology model of the enzyme derived from MMP-8. A pyrrolidinone template was selected based on an analysis of hydrogen-bonding interactions made by known MMP inhibitors and the vectors required for correct projection of established MMP binding groups (hydroxamate for Zn chelation, substituted aryl for occupation of the S1′ site). Despite the availability of several crystal structures of MMPs, few reports of their explicit use in the design of scaffolds exist.32 The novel structure of 6b, a 4-arylpyrrolidin-5-one-2-carboxylic acid hydroxyamide, represents a significant departure from those of the majority of reported MMP inhibitors. Although our work focused on inhibition of MMP-13, it seems likely that improved inhibition of other MMPs by analogues in this structural class may

be possible by optimization of the P1′ (R) group. Furthermore, the conformational rigidity of the series may be advantageous as a means to obtain selectivity. Thus 6b may be regarded as a novel, nonpeptidic, and lowmolecular-weight lead for continued pursuit of MMP inhibitors as drugs. Acknowledgment. We thank Drs. Julian Blagg, Allen J. Duplantier, Mark C. Noe, and Lawrence A. Reiter for helpful comments and reviews of the manuscript. We also thank Melissa Rockwell for enantiomeric excess determinations. References (1) Michaelides, M. R.; Curtin, M. L. Recent Advances in Matrix Metalloproteinase Inhibitor Research. Curr. Pharm. Des. 1999, 5, 787-819. (2) Whittaker, M.; Floyd, C. D.; Brown, P.; Gearing, A. J. H. Design and Therapeutic Application of Matrix Metalloproteinase Inhibitors. Chem. Rev. 1999, 2735-2776. (3) Beckett, R P.; Whittaker, M. Matrix Metalloproteinase Inhibitors 1998. Exp. Opin. Ther. Patents 1998, 8, 259-282. (4) Rothenberg, M. L.; Nelson, A. R.; Hande, K. R. New Drugs on the Horizon: Matrix Metalloproteinase Inhibitors. Oncologist 1998, 3, 271-274. (5) Bottomley, K. M.; Johnson, W. H.; Walter, D. S. Matrix Metalloproteinase Inhibitors in Arthritis. J. Enzyme Inhib. 1998, 13, 79-101. (6) MacPherson, L. J.; Bayburt, E. K.; Capparelli, M. P.; Carroll, B. J.; Goldstein, R.; Justice, M. R.; Zhu, L.; Hu, S.; Melton, R. A.; Fryer, L.; Goldberg, R. L.; Doughty, J. R.; Spirito, S.; Blancuzzi, V.; Wilson, D.; O′Byrne, E. M.; Ganu, V.; Parker, D. T. Discovery of CGS 27023A, A Non-Peptidic, Potent and Orally Active Stromelysin Inhibitor That Blocks Cartilage Degradation in Rabbits. J. Med. Chem. 1997, 40, 2525-2532. (7) During the course of this work, patent applications disclosing unrelated pyrrolidinone-based MMP inhibitors were published: (a) Jacobsen, E. J. PCT Int. Appl. WO 97/32846. (b) Duan, J.; Decicco, C. P.; Wasserman, Z. R.; Maduskuie, T. P., Jr. PCT Int. Appl. WO 99/18074.

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(8) Lovejoy, B.; Cleasby, A.; Hassell, A. M.; Longley, K.; Luther, M. A.; Weigl, D.; McGeehan, G.; McElroy, A. B.; Drewry, D.; Lambert, M. H.; Jordan, S. R. Structure of the Catalytic Domain of Fibroblast Collagenase Complexed with an Inhibitor. Science 1994, 263, 375-377. (9) Borkakoti, N.; Winkler, F. K.; Williams, D. H.; D’Arcy, A.; Broadhurst, M. J.; Brown, P. A.; Johnson, W. H.; Murray, E. J. Structure of the Catalytic Domain of Human Fibroblast Collagenase Complexed with an Inhibitor. Nat. Struct. Biol. 1994, 1, 106-110. (10) Becker, J. W.; Marcy, A. I.; Rokosz, L. L.; Axel, M. G.; Burbaum, J. J.; Fitzgerald, P. M. D.; Cameron, P. M.; Esser, C. K.; Hagmann, W. K.; Hermes, J. D.; Springer, J. P. Stromelysin-1: Three-dimensional Structure of the Inhibited Catalytic Domain and of the C-Truncated Proenzyme. Protein Sci. 1995, 4, 19661976. (11) Browner, M. F.; Smith, W. W.; Castelhano, A. L.; MatrilysinInhibitor Complexes: Common Themes among Metalloproteases. Biochemistry 1995, 34, 6602-6610. (12) Stams, T.; Spurlino, J. C.; Smith, D. L.; Wahl, R. C.; Ho, T. F.; Qoronfleh, M. W.; Banks, T. M.; Rubin, B. Structure of Human Neutrophil Collagenase Reveals Large S1′ Specificity Pocket. Nat. Struct. Biol. 1994, 1, 119-123. (13) Grams, F.; Crimmin, M.; Hinnes, L.; Huxley, P.; Pieper, M.; Tschesche, H.; Bode, W. Structure Determination and Analysis of Human Neutrophil Collagenase Complexed with a Hydroxamate Inhibitor. Biochemistry 1995, 34, 14012-14020. (14) Lovejoy, B.; Welch, A. R.; Carr, S.; Luong, C.; Broka, C.; Hendricks, R. T.; Campbell, J. A.; Walker, K. A. M.; Martin, R.; Van Wart, H.; Browner, M. F. Crystal Structures of MMP-1 and -13 Reveal the Structural Basis for Selectivity of Collagenase Inhibitors. Nat. Struct. Biol. 1999, 6, 217-221. (15) Bode, W.; Reinemer, P.; Huber, R.; Kleine, T.; Schnierer, Tschesche, H. The X-ray Crystal Structure of the Catalytic Domain of Human Neutrophil Collagenase Inhibited by a Substrate Analogue Reveals the Essentials for Catalysis and Specificity. EMBO J. 1994, 13, 1263-1269. (16) We did not have access to an X-ray crystal structure of MMP13. The model, based on MMP-8, was built using the program COMPOSER and minimized using the AMBER all-atom force field as implemented in the Sybyl program. (Sybyl 6.3, Rev 3A; Tripos Inc., 1699 Hanley Rd, Suite 303, St. Louis, MO 63144.) (17) Blake, J. F. Unpublished information. (18) Li, Y.-C.; Zhang, X.; Melton, R.; Ganu, V.; Gonnella, N. C. Solution Structure of the Catalytic Domain of Human Stromelysin-1 Complexed to a Potent, Nonpeptidic Inhibitor. Biochemistry 1998, 37, 14048-14056. (19) The (S) enantiomer is known: (a) Woo, K.-C.; Jones, K. Asymmetric Synthesis from R-Amino Acids; Some Reactions of (S)Pyroglutamate. Tetrahedron Lett. 1991, 6949-6952. (b) Shimamoto, K.; Ishida, M.; Shinozaki, H.; Ohfune, Y. Synthesis of Four Diastereomeric L-2-(Carboxycyclopropyl)glycines. Conformationally Constrained L-Glutamate Analogues. J. Org. Chem. 1991, 56, 4167-4176. (20) Johnson, C. R.; Adams, J. P.; Braun, M. P.; Senanayake, C. B. W.; Wovkulich, P. M.; Uskokovic, M. R. Direct R-Iodination of Cycloalkenones. Tetrahedron Lett. 1992, 33, 917-918. (21) In the Suzuki couplings of 8, the arylboronic acids were preferably generated from the corresponding diethanolamine complexes; see: Caron, S.; Hawkins, J. M. Directed Ortho Metalation of Neopentyl Benzoates with LDA: Preparation of Arylboronic Acids. J. Org. Chem. 1998, 63, 2054-2055.

(22) Under the Suzuki coupling conditions (aq Na2CO3/toluene/ reflux), long reaction times (>12 h) gave appreciable racemization. The use of 8 instead of the corresponding bromo lactam was preferred because the higher coupling rate allowed reaction times to be shortened to about 1 h, thus minimizing racemization as determined by chiral HPLC (ee’s > 98%). (23) Proof of the assigned stereochemistry was obtained from singlecrystal X-ray structure analysis of racemic 6f (prepared via Suzuki coupling of 8 with 3-(4-fluorophenoxy)phenylboronic acid in refluxing toluene for 16 h). Comparison of the 1H NMR spectra of 6a-e to the spectrum of 6f showed a common pattern of chemical shifts and coupling constants for the pyrrolidinone ring protons. The pattern was clearly distinguishable from that exhibited by 12. (24) Retention of the N-BOC group was essential for the success of the subsequent oxidation. (25) Zhao, M.; Li, J.; Song, Z.; Desmond, R.; Tschaen, D. M.; Grabowski, E. J. J.; Reider, P. J. A Novel Chromium Trioxide Catalyzed Oxidation of Primary Alcohols to the Carboxylic Acids. Tetrahedron Lett. 1998, 39, 5323-5326. (26) Nikam, S. S.; Kornberg, B. E.; Johnson, D. R.; Doherty, A. M. Synthesis of Hydroxamic Acids: Pd/BaSO4 as a New Catalyst for the Deprotection of O-Benzyl Hydroxamates. Tetrahedron Lett. 1995, 36, 197-200. (27) The synthesis of the 4-benzyloxyphenyl analogue 6e differed slightly by incorporation of minor changes allowing preservation of the O-benzyl ether: (1) use of EtOAc as solvent in the hydrogenation of the double bond (the benzyl ether is not hydrogenolyzed); (2) use of 2-(trimethylsilyl)ethyl (removed in the last step using BF3‚OEt2 in CH2Cl2) instead of benzyl as the hydroxamate protecting group; (3) complete removal of the BOC group prior to coupling to the hydroxylamine derivative, TMS(CH2)2ONH2‚HCl, due to partial loss of the BOC group during the H5IO6/cat. CrO3 oxidation. (28) Chen, L.; Rydel, T. J.; Gu, F.; Dunaway, C. M.; Pikul, S.; Dunham, K. M.; Barnett, B. L. Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A ¨ Resolution: Inhibitor-Induced Conformational Changes. J. Mol. Biol. 1999, 293, 545-557. (29) Kiyama, R.; Tamura, Y.; Watanabe, F.; Tsuzuki, H.; Ohtani, M.; Yodo, M. Homology Modeling of Gelatinase Catalytic Domains and Docking Simulations of Novel Sulfonamide Inhibitors. J. Med. Chem. 1999, 42, 1723-1738. (30) The isomer 12 was obtained via treatment of the intermediate corresponding to 10 with DBU (3.5 equiv) in toluene at room temperature. The epimeric product was then advanced to 12 in the usual way. (31) The acid 13 was prepared by treatment of the corresponding N-BOC compound with HCl gas in CH2Cl2. (32) Szardenings, A. K.; Harris, D.; Lam, S.; Shi, L.; Tien, D.; Wang, Y.; Patel, D. V.; Navre, M.; Campbell, D. A. Rational Design and Combinatorial Evaluation of Enzyme Inhibitor Scaffolds: Identification of Novel Inhibitors of Matrix Metalloproteinases. J. Med. Chem. 1998, 41, 2194-2200.

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